[gmx-users] Segmentation fault after warning regarding Listed nonbonded interaction

[Alexandre Barrozo]

Hey Vivek,


Thanks for the suggestion. I tried this, but I still get the same problem.


Cheers,

Alex


2014-07-17 17:58 GMT+02:00 vivek sinha <viveksinha20002 at gmail.com>:

> Hey Alex,
> I was also having the same error from two days although my topology files
> and mdp files were (I think) correct. Just two hours ago I corrected the
> problem. I just changed the timestep from 0.002 to 0.0002 and it worked.
> You can also try this.
>
> Regards,
> Vivek Sinha
>
>
> On Fri, Jul 18, 2014 at 12:42 AM, Alexandre Barrozo <barrozo.ah at gmail.com>
> wrote:
>
> > Hi everybody,
> >
> >
> > I am trying to make a simulation of an enzyme containing a metal ion
> using
> > a dummy model for it. I have inserted all the parameters, generated the
> > topology, solvated the system, without any problem.
> >
> > When I try to run a first equilibration, I get the following warning:
> >
> >
> >
> > WARNING: Listed nonbonded interaction between particles 127 and 134*
> > at distance 3f which is larger than the table limit 3f nm.
> >
> > This is likely either a 1,4 interaction, or a listed interaction inside
> > a smaller molecule you are decoupling during a free energy calculation.
> > Since interactions at distances beyond the table cannot be computed,
> > they are skipped until they are inside the table limit again. You will
> > only see this message once, even if it occurs for several interactions.
> >
> > *These particles are close to the dummy model for the metal. I believe
> the
> > problem might be related to that, but I had no problem in generating
> > topologies, or anything like that.
> >
> >
> > After that warning, I have a Segmentation fault.
> >
> >
> > Here is my mdp file for the test equilibration that I was trying:
> >
> > define                  = -DPOSRES -DPOSRES_WATER       ; position
> restrain
> > the protein
> > ; Run parameters
> > integrator              = md                            ; leap-frog
> > integrator
> > nsteps                  = 50000                         ; 2 * 50000 = 100
> > ps
> > dt                      = 0.001                         ; 1 fs
> > ; Output control
> > nstxout                 = 500                           ; save
> coordinates
> > every 1.0 ps
> > nstvout                 = 500                           ; save velocities
> > every 1.0 ps
> > nstenergy               = 500                           ; save energies
> > every 1.0 ps
> > nstlog                  = 500                           ; update log file
> > every 1.0 ps
> > ; Bond parameters
> > continuation            = no                            ; first dynamics
> > run
> > ; constraint_algorithm  = lincs                         ; holonomic
> > constraints
> > constraints             = none                          ; all bonds (even
> > heavy atom-H bonds) constrained
> > ; Neighborsearching
> > cutoff-scheme           = Verlet
> > ns_type                 = grid                          ; search
> > neighboring grid cells
> > nstlist                 = 30                            ; 20 fs, largely
> > irrelevant with Verlet
> > rcoulomb                = 1.0                           ; short-range
> > electrostatic cutoff (in nm)
> > rvdw                    = 1.0                           ; short-range van
> > der Waals cutoff (in nm)
> > ; Electrostatics
> > coulombtype             = PME                           ; Particle Mesh
> > Ewald for long-range electrostatics
> > pme_order               = 4                             ; cubic
> > interpolation
> > fourierspacing          = 0.16                          ; grid spacing
> for
> > FFT
> > ; Temperature coupling is on
> > tcoupl          = V-rescale                             ; modified
> > Berendsen thermostat
> > tc-grps         = Protein Non-Protein                   ; two coupling
> > groups - more accurate
> > tau_t           = 0.1     0.1                           ; time constant,
> in
> > ps
> > ref_t           = 1       1                             ; reference
> > temperature, one for each group, in K
> > ; Pressure coupling is off
> > pcoupl          = no                                    ; no pressure
> > coupling in NVT
> > ; Periodic boundary conditions
> > pbc             = xyz                                   ; 3-D PBC
> > ; Dispersion correction
> > DispCorr        = EnerPres                              ; account for
> > cut-off vdW scheme
> > ; Velocity generation
> > gen_vel         = yes                                   ; assign
> velocities
> > from Maxwell distribution
> > gen_temp        =  1                                    ; temperature for
> > Maxwell distribution
> > gen_seed        = -1                                    ; generate a
> random
> > seed
> >
> >
> >
> > Any clue about what is going on?
> >
> >
> > Cheers,
> >
> > Alex
> > --
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